On 24/11/2016 07:30, Christian Krause wrote:
Dear all,
I’m working as an administrator of a High-Performance Computing (HPC) Cluster
which runs on Linux. A lot of people are using R on this Linux cluster and, of
course, the *parallel* package to speed up their computations.
It has been our collective experience, that using |makeForkCluster| yields an
overall better experience /on Linux/ than the |makePSOCKcluster|, for whatever
definition of better. Let me just summarize that it works smoother. I believe,
other people working with *parallel* on Linux can share this experience
Usually, but not always. And the differences are mainly in
initialization time, so small once workers are given a reasonable amount
of work (tens of seconds each). However, as forked workers have a copy
of the whole master process, forking workers can lead to excessive
memory usage.
Also, we did really welcome the environment variable |MC_CORES|, to be able to
specify (in job submit scripts) the amount of CPU cores a user has been
granted, most importantly for /dynamic resource requests/ (see below for an
example).
Hmm, MC_CORES is primarily for mclapply() and friends, not
makeCluster(). makeForkCluster() is a 'friend' so uses it, but
makePSOCKcluster() was designed for distributing across a cluster of
machines (whereas makeForkCluster is restricted to a single multicore
machine).
What we would also appreciate - and now we finally get to the feature request -
is another environment variable to choose the used cluster, as in:
|export MC_CLUSTER_TYPE=FORK |
Do you think something like this could be implemented in future releases?
No. (Not least as 'MC_' refers to the former 'multicore' package.)
PSOCK and Fork clusters are not interchangeable, and the author of the
code has to check if Fork can be substituted for PSOCK (which starts
with a clean R environment, and that may well be assumed).
So rather, you need to ask your users to implement this in their calls
to parallel::makeCluster.
Parallel R job submit script
This works with the Univa Grid Engine and should work with other * Grid Engine
products:
|#!/bin/bash # request a "parallel environment" with 2 to 20 cores #$ -pe smp
2-20 # set number of cores for the R cluster to the granted value (between 2 and 20)
export MC_CORES=$NSLOTS # we want this: export MC_CLUSTER_TYPE=FORK Rscript
/path/to/script.R |
Best Regards
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
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